Microbiology Study Guide: Lectures 1–12 Key Concepts and Review

Lecture 1: Introduction to Microbiology

Bacterial Colonies and Their Formation

Bacterial colonies are visible clusters of bacteria that grow on the surface of solid media, such as agar plates. Each colony typically arises from a single bacterial cell or a small group of cells.

• Formation:

  • When you streak or spread bacteria onto an agar plate, individual cells become separated.

  • Each isolated cell divides repeatedly by binary fission, producing genetically identical offspring.

  • As the number of cells increases, they form a mound or cluster that becomes visible to the naked eye.

  • Pure Culture: Each colony is usually derived from a single cell, making it a pure culture of that bacterial species.

Cellular Structures Distinguishing Prokaryotes and Eukaryotes

• Prokaryotes:

  • Bacteria and Archaea

  • No membrane-enclosed organelles, no nucleus

• Eukaryotes:

  • Plants, animals, algae, protozoa, fungi

  • Contain organelles

  • DNA enclosed in a membrane-bound nucleus

Activities and Properties of Microbial Cells

Some activities and properties are common to all microbial cells, while others are only present in some.

• Common Activities:

  1. Metabolism

  2. Growth

  3. Evolution

• Additional Properties (in some cells):

  1. Motility

  2. Differentiation

  3. Communication

  4. Genetic exchange

Microbes and the Evolution of Life on Earth

• Microbes were the first forms of life on Earth.

• Key contributions:

  • Oxygen production

  • Nutrient cycling

Three Domains of Life

• Bacteria: Prokaryotic

• Archaea: Prokaryotic

• Eukarya: Eukaryotic (has a true nucleus)

Microbes in Agriculture and Food Industries

• Agriculture:

  • Nitrogen fixation

  • Decomposition: soil microbes break down organic matter, recycling nutrients for crops

  • Biocontrol: some microbes protect plants from pests and diseases

• Food Industry:

  • Fermentation

  • Food preservation

Microbes and Human Nutrition/Health

• Digestion of Complex Food:

  • Gut microbes break down dietary fibers and complex carbohydrates that our own enzymes cannot digest.

  • They produce short-chain fatty acids like acetate, propionate, and butyrate, which nourish colon cells and provide energy.

• Synthesis of Essential Nutrients:

  • Some gut bacteria synthesize vitamins that are absorbed by the host.

  • Protection against pathogens.

  • Immune system modulation.

Lecture 2: Microscopy and Spontaneous Generation

Microscopy

• Compare and contrast different types of microscopy.

• Discuss the advantages and disadvantages of staining cells prior to microscopic examination.

Spontaneous Generation and Pasteur's Experiments

• Define spontaneous generation and explain how Pasteur disproved it.

• List Koch's postulates and describe how they definitively link an agent with a specific infectious disease.

• Describe the contributions of Martinus Beijerinck and Sergei Winogradsky to the field of microbiology.

Lecture 3: Cell Structure and Diversity

• Describe and compare the structural differences of bacteria, archaea, eukaryotes, and viruses.

• What are the advantages to small cell size and what are the factors that determine the lower limits to cell size?

Lecture 4: Cytoplasmic Membrane Structure

Bacterial vs. Archaeal Cytoplasmic Membranes

• Both have a cytoplasmic (plasma) membrane that acts as a barrier and controls transport.

• Bacterial Membrane:

  • Made of phospholipids and fatty acid chains.

  • Fatty acids attached to glycerol by ester linkages.

  • Glycerol backbone is glycerol-3-phosphate.

• Archaeal Membrane:

  • Composed of isoprenoid chains (not fatty acids).

  • Isoprenoids attached to glycerol by ether linkages.

  • Glycerol backbone is glycerol-1-phosphate.

  • Some archaea have monolayer membranes for extra stability.

Additional info: Archaeal membranes are more stable in extreme environments due to ether linkages and isoprenoid chains.

Lecture 5: Cell Wall Structure

• Compare and contrast gram-positive, gram-negative, and archaeal cell wall structures.

• Discuss the composition, structure, and function of cell walls.

• What are the functional differences in cell membranes and cell walls?

Lecture 6: Capsules and Slime Layers

Capsules and Slime Layers

• Capsules:

  • Well-organized and tightly attached to the cell surface.

  • Composed mainly of polysaccharides (sometimes polypeptides).

  • Clearly visible under a microscope with special staining.

  • Help bacteria evade the immune system (by preventing phagocytosis).

• Slime Layers:

  • Loosely organized and easily washed off.

  • Appear as a diffuse, unstructured layer around the cell.

  • Both capsules and slime layers are more about protection and surface attachment, but capsules are more structured and protective, while slime layers are more about adhesion and flexibility.

Additional info: Capsules and slime layers are collectively called "glycocalyx."

Lecture 7: Prokaryotic Cell Inclusions and Gas Vesicles

• Describe the functions of various prokaryotic cell inclusions and gas vesicles.

• Describe the process of sporulation and the function it serves.

Lecture 8: Eukaryotic Cell Structures

• Describe the structures and functions of eukaryotic nuclei, mitochondria, hydrogenosomes, chloroplasts, ER, Golgi complexes, lysosomes, and cytoskeleton components.

• Explain the endosymbiotic hypothesis.

• Compare eukaryotic and prokaryotic motility structures and actions.

Lecture 9: Microbial Nutrition and Transport

• List key macro- and micronutrients required by microbes, and sources of these nutrients.

• What is active transport used for? Describe simple transport, group translocation, and ABC transport.

• Define chemotroph, chemoorganotroph, chemolithotroph, phototroph, heterotroph, and autotroph.

• Explain how $\Delta G$ and $\Delta G^\circ$ relate to endergonic and exergonic reactions.

• What is meant by "activation energy"? How do enzymes speed up chemical reactions?

Lecture 10: Redox Reactions and ATP Synthesis

• How do reduction potentials and redox reactions relate to $\Delta G$? What role do NAD+/NADH and NADP+/NADPH play in redox reactions?

• What role do high-energy bonds, ATP, and coenzyme A derivatives play in metabolism?

• Trace the components of glycolysis: What is generated by glycolysis? How do redox reactions contribute to ATP synthesis during glycolysis?

• Fermentation characteristics, what products form after steps of glycolysis are used and what is meant by fermentation vs. respiration (example: product is yeast vs. lactic acid bacteria; fermentation is different from respiration).

Lecture 11: Citric Acid Cycle and Electron Transport

• What are the purposes of the citric acid and glyoxylate cycles? What roles do the citric acid cycle and glyoxylate cycle have in common?

• What are the components of the electron transport chain? How do quinones differ from other electron carriers?

• How do electron transport reactions generate the proton motive force? How does the proton motive force generate ATP?

• How do aerobic respiration, anaerobic respiration, chemolithotrophy, and phototrophy differ? What do they have in common?

Lecture 12: Gluconeogenesis and Polysaccharide Synthesis

Gluconeogenesis and Polysaccharide Synthesis

• Gluconeogenesis: A metabolic process by which cells synthesize glucose from non-carbohydrate sources (like amino acids, lactate, or glycerol).

• Mainly occurs in the liver (in animals) and is essentially the reverse of glycolysis.

• Polysaccharides (like glycogen, starch, or cellulose) are made by linking many glucose molecules together.

• If a cell runs low on glucose from food or the environment, it must make its own glucose to build these polysaccharides.

• Gluconeogenesis provides the glucose monomers needed for the synthesis of important polysaccharides used for:

  • Energy storage (e.g., glycogen in animals, starch in plants)

  • Structural components (e.g., cellulose in plants, peptidoglycan in bacteria)

• Key Point: Without gluconeogenesis, cells couldn't make the glucose needed to build essential polysaccharides!

Summary Table: Gluconeogenesis vs. Glycolysis

Process	Main Function	Direction	Key Substrates	Key Products
Glycolysis	Breakdown of glucose to generate ATP	Glucose → Pyruvate	Glucose	Pyruvate, ATP, NADH
Gluconeogenesis	Synthesis of glucose from non-carbohydrate precursors	Pyruvate (or other precursors) → Glucose	Pyruvate, lactate, amino acids, glycerol	Glucose

Building Blocks for Macromolecules

• Where do the building blocks for amino acids, nucleotides, and fatty acids come from?

• How do bacterial and archaeal lipids differ? How are they similar?